title: Analysis of gene expression change in cancer cells induced by nucleolar stress

city: Houston

first: Han

last: Liao

address: 6431 Fannin St.

institute: The University of Texas Health Science Center at Houston

summary: Accumulating evidence indicate that aberrantly increased ribosome biogenesis is a hallmark of cancer. As such, there is a growing interest in the development of strategies to target this pathway for cancer therapeutic. It is well established that inhibition of any steps of ribosome biogenesis induces a nucleolar stress characterized by p53 activation and subsequent cell cycle arrest and/or cell death. However, cells derived from solid tumors have demonstrated different degree of sensitivity to ribosome biogenesis inhibition, where cytostatic effects rather than apoptosis are more often observed. The reason for this is not clear and the p53-specific transcriptional program induced after nucleolar stress has not been previously investigated. To investigate changes in gene expression induced by nucleolar stress we performed gene expression analysis comparing RNA from HCT116 (p53 WT) cells treated with control (duplicate experiment) vs. Las1L siRNAs (two different siRNAs).

overall_design: HCT116 cells were treated with control siRNA (in duplicate), Las1L siRNA #1 or Las1L siRNA #2 for 72 hours. Total RNAs, extracted with Trizol reagent (Invitrogen), were amplified, labeled, and hybridized to an Illumina HumanHT-12 v4 expression bead chip kit using standard protocols at The Microarray Core Lab, UT McGovern Medical School. All analyses were performed using GenomeStudio software (Illumina, Inc.).

first: Anushri

last: Gaur

first: Claire

last: Mauvais

first: Catherine

last: Denicourt


title: Study of the hypothalamic transcriptome of thermally manipulated during embryogenesis and control Japanese quails submitted or not to a heat challenge at 35 days of age

status: Public on May 20 2021

city: Nouzilly

first: Vincent

last: Coustham

address: INRAE Centre Val de Loire

country: France

institute: INRAE

type: Expression profiling by high throughput sequencing

summary: The goal of the sequencing project was to identify differentially expressed genes between four treatments (12 hypothalamus samples from quail per treatment, 6 from each sex).

overall_design: 48 quail hypothalamus RNA samples were analyzed, corresponding to 6 replicates per sex (male, female) submitted to an embryonic treatment (either TM or C) followed by a post natal treatment at 35 days of age (either RT or CH).

first: Anais

middle: V

last: Carvalho


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin [Treg]

status: Public on May 19 2021

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

country: USA

institute: University of Pittsburgh

summary: The precise mechanisms underlying the salutary effects of regulatory T cells (Tregs) on long-term tissue repair after stroke remain elusive. Here, , we performed RNAseq analysis on sorted CD4+CD25+Foxp3(GFP)+ Tregs from the ischemic brain and blood of DTR stroke mice 14d after surgery and from the blood of sham DTR mice. The unique patterns of gene expression of brain-infiltrating Tregs exhibited a significant enrichment for genes with functions in immunoregulation and cell-cell interactions, especially the activation of phagocytes.

overall_design: CD4+CD25+Foxp3+ Tregs were FACS-isolated directly into a plate with lysis buffer from the brain and blood of young male mice 14 days after transient (60 min)middle cerebral artery occlusion (tMCAO) or blood of sham operation and subjected to RNA-sequencing analysis.


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin [microglia]

summary: We cocultured Tregs in transwells with brain slices collected 5d after tMCAO in the lower compartment for 24h to activate Tregs. Tregs in the transwells were transferred to new wells with primary cultured microglia, and cocultured for 2d. Microglia were then collected for bulk RNAseq analyses. The results revealed roles of activated Tregs in polarizing microglia toward an anti-inflammatory and reparative phenotype.

overall_design: Cocultured Tregs in transwells with brain slices collected 5d after tMCAO in the lower compartment for 24h. And then Tregs in the transwells were transferred to new wells with primary cultured microglia, and cocultured for another 2d. Microglias stimulated with or without Treg were send to bulk RNAseq.


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia [RNA-Seq]

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary: RNA-seq of BCL11B overexpression in human cord blood CD34+ HSPCs identifies upregulation of T and downregulation of myeloid genes

overall_design: RNA-seq in GFP-sorted cbCD34+ cells (3 different donors) transduced with BCL11B or empty vector (EV). RNA was collected 4 days post transduction.

first: Lindsey

last: Montefiori

first: Charles

last: Mullighan


title: Transcriptome analysis using RNA sequencing of the dorsal root ganglia (DRGs) of Pink1SNCA double mutant Parkinsonian mice versus wildtype control mice

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

summary: Parkinsons's Diseases causes early pre-motor somatosensory manifestations of the disease, leading to a sensory polyneuropathy with sensory loss and chronic pain. We assessed gene gene regulation in the dorsal root ganglia (DRGs) of aged-old Pink1SNCA double mutant mice by comparing RNA-seq expression profiles. Pink1SNCA mice are a model for Parkinsons's Disease (PD) carrying a Pink1 deletion plus transgene overexpression of human mutant alpha-synuclein. Homozygous Pink1-/-,SNCA A53T double mutant mice were generated by crossing Pink1-/- mice (background: 129/SvEv) with A53T-SNCA-overexpressing mice (background: FVB/N) and then, interbreeding the littermates. They contain 129/SvEv and FVB/N genetic backgrounds approximately in a 50:50 distribution. Wildtype control mice (FVBSv) are hybrids from a crossbreeding of 129/SvEv and FVB/N mice, which were descended from littermates of double mutant mice. RNAseq was performed in two sequential experiments with 4/4 old and 4/5 aged wildytpe and Pink1SNCA mice, respectively. The alignment was done consecutively. For analysis both sets were combined. A total number of 25702 genes was reliably detected in both datasets, and 22784 passed the filtering criteria of >7 valid samples in total. GSEA gene set enrichment analysis was used for gene ranking and identication of top up- and downregulated genes and evaluation of their functions based on P-value, Q-value, fold change and abundance. Apart from the knockout of Pink1, a prominent down-regulated gene was acidic fibroblast growth factor, Fgf1, which is known to restore the survival of dopaminergic neurons in PD models. Up-regulated genes included DNase1l3, CCL27 and CCL25, IFI44 and IL31ra, and pointed to increased DNAse activity and activation of the immune system.

overall_design: RNA from the dorsal root ganglia from middle aged to old Pink1SNCA versus WT mice was analyzed by RNA sequencing of 9 and 8 biological replicates using an Illumina Next Geneneration system, NextSeq500


title: Complete loss of H3K9 methylation dissolves mouse heterochromatin organization [ChIP-seq]

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Establishment and characterization of mouse embryonic fibroblasts deficient for 6 H3K9 lysine methyltransferases (KMT)

overall_design: ChIP-seq of H3K9me1, H3K9me2, and H3K9me1 in MEFs

first: Thomas

last: Montavon

last: Jenuwein


title: Complete loss of H3K9 methylation dissolves mouse heterochromatin organization [RNA-seq 2]

summary: Establishment and characterization of mouse embryonic fibroblasts deficient for 6 H3K9 lysine methyltranswferases (KMT)

overall_design: RNA-seq of MEFs with following genotypes: wild type, Suv39h1/Suv39h2 KO, and G9a/Glp KO


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin [scRNA-seq]

summary: CD45high infiltrating immune cells were sorted from ischemic mouse brains at 5 days (5d) and 14 days (14d) after transient (60 min) middle cerebral artery occlusion (tMCAO) and subjected to scRNAseq.

overall_design: Ischemic hemispheres were harvested at 5 or 14 days after tMCAO. The CD45high cells were sorted by FACSAriaTM and send to scRNAseq.


title: Characterization of Early Gilteritinib Resistant Cell Lines

city: Portland

first: Sunil

middle: Kumar

last: Joshi

state: OR

address: 3181 SW Sam Jackson Park Rd. Mail Code: KR-HEM

department: Knight Cancer Institute

institute: Oregon Health & Science University

summary: Expression analysis performed on Early Gilteritinib Resistant cell lines vs Acute (48hr) treatment and MOLM14 Parental

overall_design: Comparison between Early Resistant and Acute as well as Early Resistant vs MOLM14 Parental

middle: K

first: Daniel

last: Bottomly

first: Shannon

last: McWeeney

first: Elie

last: Traer


title: BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia [ChIP-Seq]

summary: Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia.  We report H3K27ac and BCL11B binding in these Leukemias.

overall_design: H3K27ac and BCL11B binding in leukemia cells


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Whole-genome methylation study of congenital lung malformations in children

city: Trieste

first: Sara

last: Patrizi

address: via dell'Istria 65

country: Italy

institute: University of Trieste

type: Methylation profiling by genome tiling array

summary: The treatment of asymptomatic patients with congenital pulmonary malformations (CPMs) remains controversial, partially because the relationship between congenital lung malformations and malignancy is still undefined. Change in methylation pattern is a crucial event in human cancer, including lung cancer. We therefore studied all differentially methylated regions (DMRs) in a series of CPMs in an attempt to find methylation anomalies in genes already described in association with malignancy. The DNA extracted from resected congenital lung malformations and control lung tissue was screened using Illumina MethylationEPIC arrays. Comparison between the group of malformed samples or the malformed samples of same histology or each malformed sample and the controls, and between a pleuropulmonary blastoma (PPB) and controls were performed. All differentially methylated regions (DMRs) with an adjusted p value < 0,05 were studied. Every comparison highlighted a number of DMRs closed to genes involved either in cell proliferation or in embryonic development or included in the Cancer Gene Census. Their abnormal methylation had been already described in lung tumors. The presence of methylation abnormalities is suggestive of a correlation between congenital lung malformations and some step of malignant transformation.

overall_design: 29 total fresh-frozen paediatric lung samples: 8  healthy lung tissues, 1 Pleuropulmonary Blastoma sample, 20 Congenital Pulmonary Malformation tissues

first: Federica

last: Pederiva

first: Adamo

middle: P

last: d'Adamo


title: Genome-wide CRISPR rensensitization screens in FGF2 and FL-derived Early and Late Gilteritinib Resistant MOLM14 cultures using  Y. Kosuke library

summary: Early and late gilteritinib resistant MOLM14 cells were transduced with Cas9-blasticidin lentiviral vector to generate Cas9+-expressing cells. These cells were then infected with the Yusa CRISPR library consisting of an average of 5 single-guide RNAs (sgRNAs) per gene for 18,010 genes. After transduction, cells were selected with puromycin for 5 days to ensure stable guide integration and subjected to treatment with 100 nM of gilteritinib or vehicle (DMSO). Early gilteritinib screen cultures were maintained in 10 ng/mL of FGF2 or FL, respectively. DNA was harvested from 0-21-day cultures to amplify library of sgRNA barcodes for deep sequencing analyses. Deep sequencing of early and late resistant screens was performed on the NovaSeq and HiSeq 2500, respectively (Illumina Inc.). Genes that were significantly depleted from gilteritinib-treated cultures relative to controls were deemed essential for the survival of gilteritinib resistant cells.

overall_design: Performed comparisons of sgRNA read counts between DMSO and gilteritinib treated cells at corresponding time points. Genes that were significantly depleted from gilteritinib-treated cultures relative to controls were deemed essential for the survival of gilteritinib resistant cells.

first: Tamilla

last: Nechiporuk

first: Jeffrey

last: Tyner


title: Complete loss of H3K9 methylation dissolves mouse heterochromatin organization [ATAC-seq]

summary: Establishment and charcterization of mouse embryonic fibroblasts deficient for 6 H3K9 lysine methyltranswferases (KMT)

overall_design: ATAC-seq of MEF with following genotypes: Eset1 cKO, Eset1KO, Eset1cKO Eset2 KO, Eset1/Eset2 KO, Eset1/Suv39h1/Suv39h2 KO, Eset1/Eset2/G9a/Glp KO, Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO,  and Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO.


title: Complete loss of H3K9 methylation dissolves mouse heterochromatin organization


title: Complete loss of H3K9 methylation dissolves mouse heterochromatin organization [RNA-seq]

overall_design: RNA-seq of MEF with following genotypes: Eset1 cKO, Eset1KO, Eset1cKO Eset2 KO, Eset1/Eset2 KO, Eset1/Suv39h1/Suv39h2 KO, Eset1/Eset2/G9a/Glp KO, Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO,  and Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO.


title: BRG1 regulates neuronal activity-dependent gene activation [RNA-seq_A]

status: Public on May 18 2021

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

summary: BRG1 deletion led to impaired gene activation in neurons in response to neuronal activation

overall_design: Wildtype and Brg1-cko primary cortical neurons were treated with KCl for 6 h. Gene expression profiles were examined uisng RNA-seq

first: Jiang

last: Wu


title: BRG1 role in neuronal activity


title: Genome-wide maps of BRG1 binding sites in cortical neuron under basal and depolarized conditions [ChIP-seq]

summary: CHIP-seq analysis of BRG1 binding sites in cultured cortical neurons revealed a depolarization induced BRG1 binding to neuronal inducible enahncers.

overall_design: Culture E16.5 cortical neurons were treated with or without 50 mM KCl for one hour at 6 days in vitro. Cells were then processed using a standard protocol and subjected to ChIP-seq analyses using the J1 anti-BRG1/BRM antibody.

first: Xuanming

last: Shi


title: Open chromatin sites identified in wildtype and Brg1-cko neurons in basal and depolarized conditions [ATAC-seq]

summary: ATAC-seq analyses examined open chromatin regions in of wildtype and Brg1-cko neurons in basal and depolarized conditions.

overall_design: ATAC-seq analyses of wildtype and Brg1-cko neurons treated with or without KCl for 1 h

first: Bongwoo

last: Kim


title: Repression of endogenous retroviruses is required for mammary gland development and homeostasis [microarray]

city: Barcelona

first: Laudanna

last: Carmelo

state: Barcelona

address: Baldiri i Reixac, 10

department: Aging and Metabolism

country: Spain

institute: Institute for Research in Biomedicine (IRB-Barcelona)

summary: We demonstrate that loss of the histone H3K9 methyltransferase G9a in the developing mammary epithelium results in de novo chromatin opening which leads to severely impaired development of the mammary ductal tree, concomitant with impaired stem cell potential and disrupted intraductal polarity. Intriguingly, these phenotypes are not attributed to alterations in lineage specification and fidelity of the basal and luminal cell fates. Instead, increased chromatin opening in G9a-ablated mammary epithelium results in derepression of Long Terminal Repeat (LTR) sequences, most prominently of the ERVK family. When reverse-transcribed, these endogenous retroviruses generate double-stranded DNA (dsDNA) that accumulates in the cytosol of G9acKO mammary epithelial cells and trigger a pyroptotic antiviral innate immune response within mammary fat pads. Importantly, this altered G9acKO mammary milieu precludes functional outgrowth of even wild-type mammary stem cells upon transplantation. Our results show that tight repression of endogenous retroviruses is required for proper mammary gland development and maintenance. We demonstrate that altering chromatin accessibility of retroviral elements, as occurs during aging and cancer, severely disrupts functional mammary gland development and mammary stem cell activity through both cell autonomous and cell non-autonomous mechanisms.

overall_design: Effects of the histone H3K9 methyltransferase G9a deletion in the developing mammary gland.

first: Alexandra

last: Avgustinova

first: Carmelo

last: Laudanna


title: RNA-Seq to investigate gene expression in M. bovis BCG subjected to darG depletion or DNA damage induction with mitomycin D

city: Guildford

first: Graham

last: Stewart

address: University of Surrey

department: Faculty of Health and Medical Sciences

country: United Kingdom

institute: University of Surrey

summary: M. bovis BCG bacilli were subjected to silencing of the darG antitoxin gene by CRISPRI, leading to unregulated activity of the toxin DarT.  This results in ADP-ribosylation of specific motifs in genomic DNA, and induction of the DNA damage response.  The goal of this study is to compare gene expression of M. bovis BCG in untreated, DarG-depleted, and mitomycin treated samples.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

overall_design: Comparison of gene expression of M. bovis BCG in untreated, darG antitoxin depleted, and mitomycin C treated samples

first: Rachel

middle: E

last: Butler

middle: R

first: Huihai


title: Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with different concentrations of methionine

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

country: China

institute: Tsinghua University

summary: metR (SPD_0588) mutant (TH9197) cannot grow in  chemically defined medium (CDM) and had significant growth defect in CDM with 1  µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39.  We compared the transcriptome of WT and metR mutant in CDM with 50 µg/ml methionine by RNA-seq to see if the regulation of MetR is methionine concentration-dependdent.We also want to identify the regulon of SPD_0588 in the two RNA-seq.

overall_design: Transcriptome comparison of D39 WT and metR mutant in CDM with 1 µg/ml methionine and 50 µg/ml methionine. It was done by deep sequencing, using an Illumina Hiseq_X-TEN instrument with 150 nt paired-end reads.

first: Chengwang


title: Repression of endogenous retroviruses is required for mammary gland development and homeostasis [ATAC-Seq]

overall_design: Effects of the histone H3K9 methyltransferase G9a delition in the developing mammary gland.


title: Repression of endogenous retroviruses is required for mammary gland development and homeostasis [RNA-Seq]


title: microRNA-seq in circCDYL probe and NC probe

city: Guangzhou

first: Yun

last: Ling

address: 107 Yanjiang West Road

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: CircRNA pull-down was performed as previously reported. Briefly, SK-BR-3 was fixed with 1% formaldehyde and lysed by co-IP buffer and the cluster was sonicated. CircCDYL-specific and NC biotinylated probes were added to mixture tobind circCDYL. Next, C1 streptavidin magnetic beads was added to pull down circCDYL and circCDYL-binding RNA. Finally, total RNA was extracted from the magnetic beads and followed by qRT-PCR detection of circCDYL and miR-92b-3p.

overall_design: Examination of 2 different treatment in Breast cancer cell.

first: GeHao

last: Liang


title: Tumor immune microenvironment difference primary and metastatic hepatocellular carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: This study sought to unveil the difference of tumor microenvironment between primary and metastatic HCCs

overall_design: The immune cell composition of the matched primary and metastatic HCCs was analyzed by transcriptomic analysis.

first: C

first: D

middle: L

last: Ou


summary: In our study, we found that MetR as a transcriptional regulator may regulate the expression of genes not involved in methionine synthesis. To verify our hypothesis, we firstly construct a strain with metR over-expression in D39 and with 3×flag tag and culture this strain in chemically defined medium (CDM) without methionine. Then collect bacteria for ChIP-seq to identify the genes that can be directly transcriptionally regulated by MetR.

overall_design: ChIP-seq of Streptococcus pneumoniae D39 metR over-expression strain with 3×flag tag in CDM without methionine,  It was done by deep sequencing, using an Illumina HiSeqTM instrument with 50 nt paired-end reads.


title: microRNA profiling of the nematode Caenorhabditis elegans infected by Bacillus thuringiensis

status: Public on May 17 2021

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary: microRNAs (miRNAs) are small non-coding RNA-molecules that influence translation by binding to the target gene mRNA. Many miRNAs are found in nested arrangements within introns, or exons, of larger protein-coding host genes. miRNAs and host genes in a nested arrangement are often transcribed simultaneously, which may indicate that both have similar functions. miRNAs have been implicated in regulating defense responses against pathogen infection in C. elegans and in mammals. Here, we asked if miRNAs in nested arrangements and their host genes are involved in the C. elegans response against infection with Bacillus thuringiensis (Bt). We performed miRNA sequencing and functional genetic analysis of miRNA and/or host gene in four nested arrangements. We identified mir-58.1 and mir-2 as negative regulators of C. elegans resistance to Bt infection. However, we did not find any miRNA/host gene pair in which both contribute to defense against Bt.

overall_design: microRNA profiles of wild type (WT) C. elegans exposed to either Bacillus thuringiensis B-18247, B-18679 and B-18407 or E. coli OP50 at 2h, 6h or 12h were generated by deep sequencing (4 replicates), using Illumina HiSeq2000.

first: Alejandra

last: Zárate-Potes

first: Katja

last: Dierking


title: mRNA-profiles of Arabidopsis thaliana Col-0 (wild type) and the mutant ctl1-2 roots 14d after germination

city: Zürich

first: Susanne

last: Dora

address: Universitätsstrasse 2

department: D-Biology, Institute for molecular plant biology

country: Switzerland

institute: ETH Zürich

summary:
Background: Cell walls (CWs) are protein-rich polysaccharide matrices essential for plant growth and environmental acclimationadaptation. The CW constitutes the first physical barrier as well as a primary source of sugars for plant microbes, such as the  vascular pathogen Fusarium oxysporum (Fo). Fo colonizes roots, advancing through the plant primary CWs towards the vasculature, where it grows causing devastation in many crops. The pathogenicity of Fo and other vascular microbes relies on their capacity to reach and colonize the xylem. However, little is known about the root-microbe interaction before the pathogen reaches the vasculature and the role of the plant CW during this process.
Results: Using the pathosystem Arabidopsis-Fo5176, we show dynamic transcriptional changes in both fungus and root during their interaction. One of the earliest plant responses to Fo5176 was the downregulation of primary CW synthesis genes. We observed enhanced resistance to Fo5176 in Arabidopsis mutants impaired in primary CW cellulose synthesis. Previous studies showed an induction of ectopic lignification, accumulation of defense-related phytohormones, and dwarfism in primary CW cellulose synthesis deficient plants, potentially explaining their resistance to Fo5176. We confirmed that Arabidopsis roots deposit lignin in response to Fo5176 infection but we show that lignin-deficient mutants were as susceptible as wildtype plants to Fo5176. Genetic impairment of jasmonic acid biosynthesis and signaling did not alter Arabidopsis response to Fo5176, whereas impairment of ethylene signaling did increase vasculature colonization by Fo5176. AbolishingThis ethylene signaling interruption attenuated the observed resistance while maintaining the dwarfism observed in primary CW cellulose-deficient mutants.
Conclusions: Our study provides significant insights on the dynamic root-vascular pathogen interaction at the transcriptome level and the vital role of primary CW cellulose during defense response to these pathogens. These findings represent an essential resource for the generation of plant resistance to Fo that can be transferred to other vascular pathosystems.

last: Menna

first: Gloria

last: Sancho-Andrés

first: Clara

last: Sanchéz-Rodriguez


title: Repression of endogenous retroviruses is required for mammary gland development and homeostasis [scRNA-Seq]

first: Laudanna

last: Carmelo

first: Alexandra

first: Carmelo


title: Pharmacological Activation of STING blocks SARS-CoV-2 infection

city: Philadelphia

first: Sara

last: Cherry

address: 472A Stemmler Hall

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: We infected Calu3 cells (derived from human lung epithelium) with SARS-CoV-2 for 24 and 48 hours. Calu3 cells were also treated with the STING agonist diABZI for 6 and 12 hours. Finally, heterozygous K18-hACE c57BL/6J mice were treated with diABZI for 6 and 12 hours and lung tissue was harvested for sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Calu3 cells infected were infected with SARS-CoV-2 or treated with diABZI. Mice were treated with diABZI and lungs were harvested for sequencing.

first: Minghua

last: Li

first: Max

last: Ferretti

first: Baoling

last: Ying

first: Helene

last: Decamps

first: Emily

last: Lee

first: Mark

last: Dittmar

first: JaeSeung

first: Kanupriya

last: Whig

first: Brinda

last: Kamali

first: Holly

last: Ramage

first: Marc

last: Ferrar

first: Kristen

last: Lynch

first: Dave

last: Schultz

first: Christoph

last: Thaiss

first: Michael

middle: S

last: Diamond


title: EC-catalytic subunit dependent erythroid precursor transcriptome

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary: We tested whether Dis3 and Exosc10 depletion impact erythropoiesis by interfering with RNA processing and generating an aberrant transcriptome.

overall_design: For genome-wide transcriptomic analysis, GFP+ erythroid precursors (CD71intTer119-) and proerythroblasts (CD71int/+Ter119-) were purified from firefly luciferase, Dis3 or Exosc10 shRNA-expressing fetal liver cells. RNA-seq was conducted in quadruplicate with RNA isolated from cells sorted 2 days after culture in erythroid expansion media.

first: Charu

last: Mehta

middle: N

first: Emery

middle: H

last: Bresnick


title: mRNA-profiles of Arabidopsis thaliana (Col-0) roots infected with Fusarium oxysporum 5176 over a time course of six days

first: Susanne

last: Dora

sample_organism:
Arabidopsis thaliana
Fusarium oxysporum

platform_organism:
Arabidopsis thaliana
Fusarium oxysporum

first: Alexandra

last: Menna

first: Gloria

last: Sancho-Andrés

first: Clara

last: Sanchéz-Rodriguez


title: Gene expression data of alveolosphere/airway organoid and alveolosphere with SARS-CoV-2 or mock infection

city: Shinjuku-ku

first: Toshiki

last: Ebisudani

state: Tokyo

address: Shinanomachi 35

department: Organoid medicine

country: Japan

institute: Keio University

summary: Although the main cellular target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is thought to be alveolar cells, the absence of their tractable culture system has precluded the development of a clinically-relevant SARS-CoV-2 infection model. Here, we established an efficient human alveolosphere culture method and sphere-based drug testing platform for SARS-CoV-2. Alveolospheres exhibited indolent growth in a Wnt and R-spondin dependent manner. Gene expression, immunofluorescence and electron microscopy analyses revealed the presence of alveolar cells in alveolospheres. Alveolospheres expressed ACE2 and allowed SARS-CoV-2 to propagate nearly 100,000- fold in three days of infection. While lopinavir and nelfinavir, protease inhibitors used for the treatment of HIV infection, had a modest anti-viral effect on SARS-CoV-2, remdesivir, a nucleotide prodrug, showed anti-viral effect at the concentration comparable to the circulating drug level. These results demonstrated the validity of alveolosphere culture system for the development of therapeutic agents to combat SARS-CoV-2.

overall_design: 1. mRNA profiles of alveolosphere and airway organoid  2. mRNA profiles of alveolosphere with SARS-CoV-2 or mock infection at 2dpi

first: Shinya

last: Sugimoto

first: Toshiro

last: Sato


title: A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual-transcriptomics

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Discerning role of a functional arsenic resistance cassette in evolution and adaptation of a rice pathogen

city: Chandigarh

first: Prabhu

middle: B

last: Patil

state: Chandigarh

address: Sector 39 A

country: India

institute: CSIR Institute of Microbial Technology Chandigarh

summary: Arsenic (As) is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification, and adaptation mechanisms in bacteria that are associated with host in arsenic-rich conditions can provide novel insights into dynamics of host-microbe-microenvironment interactions.  In the present study, we have investigated an arsenic resistance mechanism acquired during the evolution of a particular lineage in the population of Xanthomonas oryzae pv. oryzae (Xoo), which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12kb ars cassette in Xoo IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. This cassette has spread in lineage with highly virulent strains owing to a particular lineage’s evolutionary success. Further, we performed the transcriptomic analysis of Xoo strain IXO1088 under arsenate/arsenite exposure using RNA sequencing. The transcriptomic analysis revealed that arsenic detoxification and efflux, oxidative stress response, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. The study provides useful insights into the acquisition, detoxification, and adaptation mechanisms among Xoo populations to adapt under arsenic-rich environmental conditions.

overall_design: Transcriptional response of Xanthomonas oryzae pv. oryzae IXO1088 under arsenate [As (V)] (0.5mM and 1mM) and arsenite [As (III)] (0.6mM) exposure.

first: Amandeep

last: Kaur

first: Rekha

last: Rana

first: Tanu

last: Saroha


title: Genetic and molecular determinants of polymicrobial interactions in Fusobacterium nucleatum

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

summary: A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions –termed coaggregation–by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. Here, we employed genome-wide transposon mutagenesis to uncover fusobacterial coaggregation factors, revealing the intertwined functionof a two-component signal transduction system (TCS), named CarRS, and a lysine metabolic pathway in regulating the critical coaggregation factor RadD. Transcriptome analysis shows that CarR modulates a large regulon including radD and lysine metabolic genes, such as kamA and kamD, the expression of each which is highly up-regulated in the ΔcarR mutant. Significantly, the native culture medium of ΔkamA or ΔkamD mutants builds up abundant amounts of free lysine, which blocks fusobacterial coaggregation with streptococci. Our demonstration that lysine-conjugated beads trap RadD from the membrane lysates suggests that lysine utilizes RadD as its receptor to act as a metabolic inhibitor of coaggregation. Lastly, using a mouse model of preterm birth, we show that fusobacterial virulence is significantly attenuated with the ΔkamA and ΔcarR mutants, in contrast to the enhanced virulence phenotype observed upon diminishing RadD (ΔradD or ΔcarS mutant). Evidently, F. nucleatum employs the TCS CarRS and environmental lysine to modulate RadD-mediated interspecies interaction, virulence, and nutrient acquisition to thrive in the adverse environment of oral biofilms and extraoral sites.

sample_organism: Fusobacterium nucleatum subsp. nucleatum

overall_design: Examination of carR deficient mutant compared to parental strain in biological triplicates

first: Chenggang

last: Wu

first: Yi-Wei

last: Chen

first: Matthew

last: Scheible

first: Chungyu

last: Chang

first: Ju

last: Huck Lee

first: Truc

middle: T

last: Luong

first: Bethany

last: Tiner

first: Andreas

last: Tauch

first: Asis

last: Das

first: Hung

last: Ton-That


title: THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE]

city: Pittsburgh

first: Jeffrey

last: Gross

department: Ophthalmology

institute: University of Pittsburgh School Of Medicine

summary: Loss of the retinal pigment epithelium (RPE) due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self-repair is an attractive therapeutic strategy; however, mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues, including the RPE, but little is known about the mechanisms that drive RPE regeneration. Here, utilizing zebrafish, we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post-RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro-regenerative environment in mammals.

overall_design: RNA-seq from FACS-purified retinal pigment epithelium (RPE) post-genetic ablation and in unablated controls at 3 timepoints: 2, 4, 7 days post-injury (dpi). MTZ- indicates unablated samples, MTZ+ indicates ablated samples.

first: Lyndsay

last: Leach

middle: M


title: THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [macrophages]

overall_design: RNA-seq from FACS-purified macrophages/microglia post-genetic ablation of the retinal pigment epithelium and in unablated controls at 2 timepoints: 2 and 4 days post-injury (dpi). MTZ- indicates unablated samples, MTZ+ indicates ablated samples.


title: Chromatin Landscape of IL-4-expressing CD4 T cells in the lung and lung-draining lymph nodes

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

summary: Using bulk-, single cell-, ATAC-, and TCR repertoire sequencing, this study reveals that helminth infection causes the expansion of distinct IL-4-competent CD4+ T cells in the lung and lung-draining lymphoid tissues, providing insight into tissue-specific mechanisms of type-2 cytokine regulation and the lineage commitment of T-helper 2 (Th2) and T follicular helper (Tfh) cells. IL-4 competent CD4+ T cells were stratified into three groups: lymphoid-restricted T follicular helper (Tfh) cells; nonlymphoid resident T-helper 2 (Th2) cells; and transitional cells that share identity with both tissue compartments. Differences in transcriptome, locus accessibility, and the enrichment of distinct transcription factor motifs suggested that IL-4 competency was likely achieved via distinct mechanisms among lymphoid- and lung-resident CD4+IL-4+ populations. These findings reveal a complex relationship between lymphoid- and nonlymphoid-resident CD4+ T cell populations in settings of type-2 immunity.

overall_design: Genome-wide ATAC-sequencing was used to profile regulatory regions in 3 distinct CD4+ T cell subsets that arise in lymphoid and nonlymphoid tissues after N. brasiliensis infection.

first: Thomas

last: Danhorn

first: James

last: Scott-Browne

first: Brian

last: O'Connor

first: Laura

last: Harmacek

first: Cydney

last: Rios

first: Rachel

last: Woolaver

first: Sonia


title: Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets II

city: Southampton

first: Michaela

last: Reichmann

address: Tremona Road

institute: University of Southampton

summary: We hypothesised that whole transcriptome analysis of human TB granulomas isolated by laser capture microdissection could identify therapeutic targets, and that comparison with a non-infectious granulomatous disease, sarcoidosis, would identify disease-specific pathological mechanisms.  Bioinformatic analysis of RNAseq data identified numerous shared pathways between TB and sarcoidosis lymph nodes, and also specific clusters demonstrating TB results from a dysregulated inflammatory immune response.  To translate these insights, we compared three primary human cell culture models at the whole transcriptome level, and demonstrated that the 3D collagen granuloma model most closely reflected human TB disease. We investigated shared signaling pathways with human disease and identified twelve intracellular enzymes as potential therapeutic targets.  Sphingosine kinase 1 inhibition controlled Mtb growth, concurrently reducing intracellular pH in infected monocytes and suppressing inflammatory mediator secretion.  Immunohistochemical staining confirmed that sphingosine kinase 1 is expressed in human lung TB granulomas, and therefore represents a host therapeutic target to improve TB outcomes.

overall_design: Thirty-six cell culture conditions in total.  PBMCs from six healthy donors cultured in uninfected and Mtb infected models: 2D culture; 3D alginate microsphere; and 3D collagen microspheres.


title: Total RNA sequencing of the liver tissues of Oreochromis niloticus (Nile Tilapia) and of Pundamilia nyerei

city: Cambridge

first: Sudhakaran

last: Prabakaran

address: Downing Site, CB2 3EH, UK

department: Department of Genetics

institute: University of Cambridge

summary: Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). Our results suggest that the time scale of speciation of the two species can be better explained by the evolutionary divergence of these nORF genomic regions.

sample_organism:
Oreochromis niloticus
Pundamilia nyererei

overall_design: Total RNA was extracted from liver tissue of two cichlid fishes: Oreochromis niloticus and Pundamilia nyererei; three samples each.

first: Shraddha

last: Puntambekar

last: Newhouse

first: Jaime

last: Navas

first: Ruchi

last: Chauhan

first: Grégoire

last: Vernaz

last: Willis

first: Matthew

last: Wayland

first: Yagnesh

last: Urmania

first: Eric

middle: A

last: Miska


title: Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

summary: Programmed ribosomal frameshifting is the key event during translation of the SARS-CoV-2 RNA genome allowing synthesis of the viral RNA-dependent RNA polymerase and downstream viral proteins. Here we present the cryo-EM structure of the mammalian ribosome in the process of translating viral RNA paused in a conformation primed for frameshifting. We observe that the viral RNA adopts a pseudoknot structure lodged at the mRNA entry channel of the ribosome to generate tension in the mRNA that leads to frameshifting. The nascent viral polyprotein that is being synthesized by the ribosome paused at the frameshifting site forms distinct interactions with the ribosomal polypeptide exit tunnel. We use biochemical experiments to validate our structural observations and to reveal mechanistic and regulatory features that influence the frameshifting efficiency. Finally, a compound previously shown to reduce frameshifting is able to inhibit SARS-CoV-2 replication in infected cells, establishing coronavirus frameshifting as target for antiviral intervention.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Ribosome profiling of SARS-CoV-2 in-vitro translation

first: Pramod

last: Bhatt

first: Alain

last: Scaiola

first: Gary

last: Loughran

first: Marc

last: Leibundgut

first: Annika

last: Kratzel

first: Angus

last: McMillan

first: Kate

last: O’ Connor

first: Jeffrey

middle: W

last: Bode

first: Volker

last: Thiel

first: John

middle: F

last: Atkins

first: Romane

last: Meurs

first: David

last: Gatfield

first: Nenad

last: Ban


title: Transcription profiling of IL-4-expressing CD4 T cells in the lung and lung-draining lymph nodes

first: Richard

last: Reinhardt

summary: Using single cell RNA-sequencing and whole-genome targeted transcription profiling, this study reveals that helminth infection causes the expansion of distinct but clonally related IL-4-competent CD4+ T cells in the lung and lung-draining lymphoid tissues providing insight into tissue-specific mechanisms of type-2 cytokine regulation and the lineage commitment of T-helper 2 (Th2) and T follicular helper (Tfh) cells.

overall_design: Genome-wide targeted sequencing to profile transcription of 4 distinct CD4+ T cells in lymphoid and nonlymphoid tissues

first: Max

last: Seibold

first: Nathan

last: Dyjack


title: Transcriptional analysis of SARS-CoV-2 specific CD4 T cells

status: Public on May 16 2021

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: The objective of this analysis was to determine if there was a transcriptional difference in the CD4 T cell response elicited by SARS-CoV-2 infection in individuals that quickly resolved their infection compared to those individuals with prolonged SARS-CoV-2-associated symptoms

overall_design: A total of PBMC 10 samples from convalescent COVID-19 patients were stimulated in vitro with SARS-CoV-2 Spike protein peptide pools overnight. Spike-reactive CD4 T cells were identified by merit of their upregulation of CD69 and CD134 in response to peptide stimulation. Antigen-specific cells were sorted directly into RLT+ lysis buffer for transcriptional analysis


title: Exploration of exhausted CD8 T cell markers to predict response to immune checkpoint inhibitor therapy for hepatocellular carcinoma

first: Chia-Lang

last: Hsu

summary: This study sought to identify transcriptomic and protein markers of T cell exhaustion that may predict response to anti-program cell death-1 (anti-PD-1) / anti-PD-L1-based ICI therapy for patients with advanced/metastatic hepatocellular carcinoma (HCC).

overall_design: The immune cell composition of archival HCC tumor who received ICI therapy was analyzed by transcriptomic analysis to identify markers of T cell exhaustion that best associated with treatment efficacy.

first: C

first: D

last: Ou


title: Zebrafish (Danio rerio) Schwann cell, oligodendrocyte lineage, and neuron RNA-sequencing

status: Public on May 15 2021

city: Charlottesville

first: Sarah

last: Kucenas

state: VA

address: 90 Galderd Dr, Rm 312

department: Biology

institute: University of Virginia

summary: RNA-sequencing of cells collected from 72 hpf embryos: Schwann cells (Gt(foxd3:mCherry);Tg(sox10:mEGFP)), oligodendrocyte lineage cells (Tg(olig2:dsred);Tg(sox10:megfp)), and neurons (Tg(nbt:dsred))

overall_design: Cells were collected from 72 hpf embryos as follows and sent for sequencing. For Schwann cells, foxd3+/sox10+ double positive cells were collected from trunks of Gt(foxd3:mCherry);Tg(sox10:mEGFP) embryos. For oligodendrocyte lineage cells, olig2+/sox10+ double positive cells were collected from the trunks of Tg(olig2:dsred);Tg(sox10:megfp) embryos. For neurons, nbt+ cells were collected from the trunks of Tg(nbt:dsred) embryos. 3 replicates for each condition.

first: A

middle: J

last: Latimer

first: M

last: Piller

first: S


title: Development of β-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease

city: Stanford

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: The pre-clinical efficacy and safety data support the initiation of a phase I/II clinical trial for β-globin gene correction in patient-derived hematopoietic stem cells for the treatment of sickle cell disease.

overall_design: This entry covers wild type and high fidelity Cas9 genome-wide repair outcomes from the HBB locus using LAM-HTGTS.

first: Annalisa

last: Lattanzi

first: Joab

last: Camarena

first: Premanjali

last: Lahiri

first: Helen

last: Segal

first: Waracharee

last: Srifa

first: Christopher

last: Vakulskas

first: Josefin

last: Kenrick

first: Ciaran

last: Lee

first: Narae

last: Talbott

first: Jason

last: Skowronski

middle: K

last: Cromer

first: Carsten

last: Charlesworth

first: Rasmus

middle: O

last: Bak

first: Gang

last: Bao

last: DiGiusto

last: Tisdale

first: J

last: Wright

first: Neehar

last: Bathia

first: Maria

middle: G

last: Roncarolo

first: Daniel

last: Dever

first: Matthew

last: Porteus


title: Difference between sulforaphane and sulforaphene in colon cancer

city: Jinan

first: Fengying

last: Du

state: China

address: jingwuweiqi street, 324

institute: Shandong Provincial Hospital

summary:
Sulforaphane and sulforaphene are isothiocyanate compounds derived from cruciferous vegetables that have demonstrated antiproliferative properties against colon cancer. However, the underlying mechanism of action of these two compounds is yet to be elucidated.
The present study aimed to study the effects of sulforaphane and sulforaphene on colon cancer by next-generation sequencing (NGS).

overall_design: The colon cancer cell line, SW480, was cultured with 25 μmol/l sulforaphane and sulforaphene. Total RNA was extracted following 48 h of incubation of the cells with the compounds and NGS was performed with Clariom S Array.

first: Yutao

last: Wang


title: Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets

first: Michaela

last: Reichmann

overall_design: Laser microdissection of FFPE mediastinal and neck lymph node granulomas of seven untreated TB patients, FFPE mediastinal lymph node granulomas of ten untreated sarcoidosis patients, and FFPE mediastinal reactive lymph node tissue of seven newly diagnosed cancer patients prior to therapy.


title: The transcriptome of 2 pairs of monozygotic twins clinically discordant for IgA nephropathy

city: Beijing

first: min

last: wei

address: No 8, Xishiku Street

institute: perking university First Hospital

summary: Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis involves both genetic and environmental factors. DNA methylation, the most studied epigenetic modification, was shown to play a role in IgAN. In two pairs of IgAN-discordant monozygotic (MZ) twins, here we assessed genome-wide DNA methylation profiling and gene expression profiling in order to characterize DNA methylation changes in IgAN and their potential influences on gene expression.

overall_design: Genome-wide DNA methylation and gene expression profiles were evaluated in peripheral blood mononuclear cells (PBMCs) obtained from two MZ twins discordant for IgAN. Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected and an integrated analysis was performed.

first: Min

last: Wei

first: Sijun

last: Meng

first: Sufang

last: Shi

first: Lijun

last: Liu

first: Xujie

last: Zhou

first: Jicheng

last: Lv

first: Li

last: Zhu

first: Hong

last: Zhang


title: The transcriptome and genome-wide DNA methylation data of 2 pairs of monozygotic twins clinically discordant for IgA nephropathy

type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series


title: Genome-wide DNA methylation data of 2 pairs of monozygotic twins clinically discordant for IgA nephropathy


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell_Intra]

status: Public on May 14 2021

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels.  Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.

overall_design: Sorted human T-cells from one biological donor were activated and target genes were perturbed using CRISPR / Cas9. Gene KOs were generated in a pooled fashion using gRNAs targeting CD69, CTLA4, IFNG, MKI67, CD28, CD45, PD1, CD4, CD3E, ZAP70 with two non-targeting controls. Changes in chromatin accessibility and protein abundance were determined concomitantly in single cells.

first: Eleni

last: Mimitou

first: Kelvin

last: Chen

first: Leif

last: Ludwig

first: Peter

last: Smibert


title: BRG1 S1382 phosphorylation regulates neuronal activity-dependent gene activation [RNA-seq_B]

city: Richardson

first: Zhenyu

last: Xuan

address: 800 West Campbell

institute: UT Dallas

summary: BRG1 S1382 phospho-mutations led to altered gene activation in neurons in response to neuronal activation

overall_design: Wildtype and Brg1-S1382A or Brg1-S1382E knock-in primary cortical neurons were treated with KCl for 1 h. Gene expression profiles were examined uisng RNA-seq

first: Jiang

last: Wu

first: Bongwoo

last: Kim

first: Yi

last: Luo


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC_Stim_Multiome]

overall_design: Control and stimulated with aCD3/CD28 PBMC samples were stained with a 210-antibody panel and used to apply DOGMA-seq to simultaneously measure changes in protein, mRNA levels, and chromatin accessibility in the same individual cells.


title: Profiling the Small Non-coding RNA Transcriptome of the Human Placenta

city: Vancouver

first: Wan

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

summary: Proper functioning of the placenta, the temporary organ crucial in fetal development during pregnancy, is critical for maternal and fetal health. While microRNAs (miRNAs) are known to impact placental gene expression, the effects of other small non-coding RNAs (sncRNAs) on the placental transcriptome are not well-established. Here, we performed small RNA sequencing of 30 chorionic villi samples of varying gestational ages (M = 23.5 ± 11.4 weeks). We observed expression of 1543 sncRNAs, including miRNAs, piRNAs, snRNAs, snoRNAs, and tRNAs, as well as 18,003 miRNA variants (isomiRs), and identified 48 previously-unannotated miRNAs. This novel characterization of the placental sncRNA transcriptome may aid future investigations of sncRNA regulatory functions within the human placenta.

overall_design: A total of 30 samples were obtained from first trimester, second trimester, and term pregnancies. First trimester samples were obtained after elective terminations. Second trimester samples were obtained after fetal demise conditions. Six of these second trimester samples were classified as having neural tube defects. After RNA extraction, samples were sequenced at Canada’s Michael Smith Genome Sciences Centre, in Vancouver.


title: Molecular mechanisms of Guadecitabine induced FGFR4 down regulation in alveolar rhabdomyosarcomas

city: Los Angeles

first: Emad

last: Darvishi

state: CA

address: 4650 Sunset Blvd

department: Cancer and Blood Disease Institute

institute: Children’s Hospital Los Angeles

summary: Fibroblast growth factor receptor 4 (FGFR4) aberrant expression and activity have been linked to the pathogenesis of a variety of cancers including rhabdomyosarcomas (RMS). We found that treatment of alveolar rhabdomyosarcoma (aRMS) cells with Guadecitabine (SGI-110), a next-generation DNA methyltransferase inhibitor (DNMTi), resulted in a significant reduction of FGFR4 protein levels, 5 days post treatment. Chromatin immunoprecipitation-sequencing (ChIP-seq) in aRMS cells revealed attenuation of the H3K4 mono-methylation across the FGFR4 super enhancer without changes in tri-methylation of either H3K4 or H3K27. These changes were associated with a significant reduction in FGFR4 transcript levels in treated cells. These decreases in H3K4me1 in the FGFR4 super enhancer were also associated with a 240-fold increase in KDM5B (JARID1B) mRNA levels. Immunoblot and immunofluorescent studies also revealed a significant increase in the KDM5B protein levels after treatment in these cells. KDM5B is the only member of KDM5 (JARID1) family of histone lysine demethylases that catalyzes demethylation of H3K4me1. These data together suggest a pleiotropic effect of DNMTi therapy in aRMS cells, converging to significantly lower FGFR4 protein levels in these cells.

overall_design: Examination of 3 different histone marks enrichment across the FGFR4 super enhancer post Guadecitabine treatment in RH30 cell line.

first: Lee

last: Helman


title: Oncogene-induced senescence in hematopoietic progenitors features myeloid restricted hematopoiesis, chronic inflammation and histiocytosis

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: We generated a humanized mouse model of oncogene-induced senescence in hematopoietic stem and progenitor cells by expressing the activated oncogene BRAF-V600E. Mice succumbed to bone marrow failure and multi-organ dissemination of aberrant macrophages and dendritic cells. We observed a myeloid-restricted hematopoiesis,and uncovered the activation of a senescence program, characterized by growth arrest and senescence-associated secretory phenotype (SASP), which involved  also non-mutated bystander cells.

overall_design: We sequenced the mRNA of FACS-sorted human CD45+CD33+ cells from the bone marrow of NSG mice transplanted with CD34+ cells transduced with lentiviral vectors expressing BRAF-V600E and GFP, wtBRAF and GFP, GFP alone and mock control

first: Riccardo

last: Biavasco

first: Emanuele

last: Lettera

first: Ivan

last: Merelli

first: Raffaella

last: Di Micco

first: Eugenio

last: Montini


title: Renal Epo producing Sca-1+ interstitial cells are increased in number after treatment with the anemia drug roxadustat

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We identify and analyse in detail a specific Sca-1-positive cell population that increases after treatment with the anaemia drug roxadustat and is capable to support Epo production in mice

overall_design: Comparison of freshly isolated cells of roxadustat-treated and untreated mice with cells maintained in roxadustat-complemented culture for seven and 21 days including the respective controls

first: Dörthe

last: Katschinski

first: Aline

last: Jatho


title: Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR3 and TLR7 activation in Bone-marrow-derived macrophage

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

institute: Academia Sinica

summary: The goal of this study is to compare gene expression between TLR3 and TLR7

overall_design: The BMDM were treated poly(I:C) or CL075 for 6hr for activation. The total RNAs were extracted for deep sequencing, in triplicate, using the NextSeq500 High-output v2 (75 cycle) sequencing kit on the Illumina NextSeq500 instrument.

first: Yun-Fen

last: Hung

first: Chiung-Ya

last: Chen


title: Mediator of DNA damage checkpoint 1 (MDC1) is a novel estrogen receptor co-regulator in invasive lobular carcinoma of the breast

status: Public on May 13 2021

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: We identified MDC1 as a putative novel transcriptional co-regulator of estrogen receptor alpha (ER) in models of invasive lobular carcinoma. In this study, our goal was to define the contribution of MDC1 to regulation of the ER transcriptome in ILC cell lines versus invasive ductal carcinoma cells.

overall_design: RNAseq was used to examine estrogen-driven changes in gene expression, with or without knockdown of MDC1, ER, or FOXA1. We compared gene expression in invasive lobular carcinoma cell lines (MM134/MDA MB 134VI, MM330/MDA MB 330) to invasive ductal carcinoma cell line HCC1428.

first: Matthew

last: Sikora

first: Evelyn

last: Bordeaux

first: Joseph

last: Sottnik

first: Sanjana

last: Mehrotra

middle: E

first: Sarah

last: Ferrara

first: James

middle: C

last: Costello


title: Anti-aging effect of olmesartan on miRNA expression profile in smooth muscle cells

city: Guangzhou

first: Li

last: Zhang

state: Guangdong

address: No. 19, Nonglinxia Road

institute: The First Affiliated Hospital of Guangdong Pharmaceutical University

summary: High-throughput sequencing technique was used to screen the miRNAs which has potential role in the aging delaying effect of olmesartan on human smooth muscle cells. We cultured human vascular smooth muscle cells and used the third to fifth generation cells as unaging cells (Zhengchang-1,-2,-3), natural culture to passage 10 to 15 as aging group samples (Bo-1,-2,-3), and cells treated with olmesartan for the same time as aging group cells as treatment group (bo-ao-1,-2,-3). After collecting cells of each group, RNA was extracted and reversed. After the quality inspection was qualified, miRNA sequencing was carried out. Finally, we confirmed that the miRNA expression profile of human vascular smooth muscle cells changed after olmesartan treatment. This study confirmed that miRNA plays a potential role in the aging process of human smooth muscle cells and that olmesartan may play a role in delaying aging by regulating miRNA expression profile.

overall_design: Examination the miRNAs profiles in Olmesartan-treated human Senescent VSMCs


title: Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq]

city: Iowa City

last: Voigt

state: Iowa

address: 375 Newton Road

institute: University of Iowa

summary:
Purpose: The goals of this study were to identify expression patterns in foveal versus parafoveal cells isolated from the human retina.
Methods: Independent libraries were prepared for foveal and parafoveal cells isolated from four human donors (donors 5-8). A foveal (1 mm) and parafoveal (4 mm) punch of neural retina was acquired from each donor. Each punch of neural retina was gently dissociated in papain (Worthington biochemical) for 1.25 hours before cryopreservation. Thawed cells were barcoded with the 10X chromium and resulting libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build GRCh38 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from single-cell donors 5-8 were aggregated using canonical correlation analysis. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1).
Results: A total of 34,493 cells were recovered after filtering with 139,962,070 corresponding reads. A total of 5,856 cells were recovered from foveal libraries while 28,637 cells were recovered from the parafoveal libraries. Clusters were assigned to known retinal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from the fovea versus the parafovea. Particular emphasis was given to regionally expressed genes in cone photoreceptor cells and Muller cells.
Conclusions: This study provides a transcriptomic comparison of the foveal and parafoveal human retina at the bulk and single-cell levels. The foveal retina is transcriptomically distinct from the directly surrounding parafovea.

overall_design: mRNA profiles for thousands of cells from foveal and parafoveal retina were generated from four human donor eyes (single-cell donors 5-8) using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina NovaSeq.

first: Todd

last: Scheetz

middle: P

first: Robert

last: Mullins


title: YAP1 nuclear efflux and transcriptional reprograming is triggered by membrane diminution upon VSV-G-induced cell fusion

city: Ashburn

first: Daniel

last: Feliciano

address: 19700 Helix Dr

institute: Janelia, HHMI

summary: Cells in many tissues, such as bone, muscle, and placenta, fuse into syncytia to acquire new functions and transcriptional programs. While it is known that fused cells are specialized, it is unclear whether cell-fusion itself promotes programmatic changes that generate the new cellular state. To address this, we employed a fusogen-mediated, cell-fusion system to create syncytia from undifferentiated cells. RNA-seq analysis revealed cell-fusion initiates dramatic transcriptional changes. To gain mechanistic insights, we measured plasma membrane surface area after cell-fusion and found it diminished through increased endocytosis. Consequently, glucose transporters are internalized, and cytoplasmic glucose and ATP transiently decrease. This reduced energetic state activates AMPK, which inhibits YAP1, causing extensive transcriptional- reprogramming and cell-cycle arrest. Impairing either endocytosis or AMPK activity prevents YAP1 inhibition and cell-cycle arrest after fusion. Together, these data demonstrate plasma membrane diminishment upon cell-fusion causes transient nutrient stress that promotes transcriptional-reprogramming independent from extrinsic cues.

overall_design: Eight total samples of SUM-159 cells were analyzed using RNA-seq.  There are four replicates of control cells and four replicates of VSV-G mediated fused cells

first: Jennifer

last: Lippincott-Schwartz


title: Human photoreceptor cells from different macular subregions have distinct transcriptional profiles

summary: This SuperSeries is composed of the SubSeries listed below.


title: YTHDF1 suppresses innate immune responses by promoting induction of A-to-I RNA editing

city: Chicago

first: Hideki

last: Terajima

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: In this study, we show that the m6A modification promotes translation of the ADAR1 transcript, which encodes an A-to-I RNA editing enzyme, in response to interferon stimulation. We reveal that this translation upregulation is mediated by the YTHDF1-dependent pathway; YTHDF1 is a reader protein that can preferentially bind m6A-modified transcripts and promote translation. Knockdown of YTHDF1 reduces the overall levels of interferon-induced A-to-I RNA editing, which consequently activates dsRNA-sensing pathway and increased expression of various interferon-stimulated genes. These RNA-seq experiments investigate the effect of YTHDF1 knockdown on the interferon-treated A172 cell transcriptome.

overall_design: mRNA profiles of A172 glioblastoma cells with IFN treatment and YTHDF1 knockdown were generated by deep sequencing, in triplicate.

first: Chuan

last: He


title: Prostaglandin E2 (PGE2) Enhances Aged Hematopoietic Stem Cell Function

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

state: IN

address: 980 W. Walnut St.

department: Medicine

institute: Indiana University School of Medicine

summary: The purpose of this RNA sequencing dataset was to analyze transcriptional signaling in young and aged murine hematopoietic stem cells when pulsed ex vivo with dimethyl (dm)PGE2.

overall_design: RNS sequencing was performed on hematopoietic stem cells isolated from young (n=4) or aged (n=4) mice and pulsed ex vivo with dmPGE2 or vehicle (note: each sample was split in two for matched analysis of dmPGE2 vs vehicle effects).

first: Christie

last: Orschell


title: Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [bulk RNA-seq]

summary:
Purpose: The goals of this study were to identify cell specific expression patterns from the fovea, perifovea, and macular neural retina.
Methods: Independent libraries were prepared for human foveal (1mm), perifoveal (4mm), and macular (8mm) regions of neural retina. Poly-A selected RNA transcripts underwent 150 base-pair paired-end sequencing with an Illumina HiSeq 4000. Reads were mapped to the human genome hg19 with STAR (version = 020201) and quantified with the featureCounts function from the Rsubread package (version = 1.28.1). Differential expression analysis was performed with edgeR (version = 3.26.8).
Results: Differential expression analysis identified genes enriched in each retinal region.
Conclusions: This study provides a transcriptomic comparison of foveal, perifoveal, and macular human neural retina at the bulk and single-cell levels.

overall_design: mRNA profiles from human neural retina isolates were generated from four donor eyes followed by sequencing on a HiSeq 4000.


title: Cytokine profile of mature WT bone marrow-derived dendritic cells and fascin1 knockout bone marrow-derived dendritic cells

status: Public on May 12 2021

city: Piscataway

first: Fumio

last: Matsumura

address: 604 Allison Rd

department: MBB

institute: Rutgers

summary: Cytokines secreted by WT and fascin1 KO BM-DCs maturated by LPS were determined by RayBio Quantibody mouse Th17 array1.  Fascin1 KO BM-DCs show reduced  secretion of several cytokines including IL-6.

overall_design: For analyses of cytokines in culture supernatants of BMDCs, WT and fascin1 KO BMDCs were cultured overnight after addition of LPS (100ng/ml).  Culture supernatants were then used for profiling of inflammatory cytokines using a RayBio Quantibody mouse Th17 array1 according to the manufacturer’s instructions (RayBiotech).  The Quantibody array allows us to quantitatively determine the concentrations of 18 cytokines/chemokines (IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12 p70, IL-17, IL17F, IL-21 IL-22, IL-23, IL-28, IFN, MIP-3, TGF1, and TNF).

first: Shigeko

last: Yamashiro


title: Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s Disease

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

summary: The gene-regulatory landscape of the brain is highly dynamic in health and disease, coordinating a menagerie of biological processes across¬ distinct cell-types. Here, we present a multi-omic single-nucleus study of 191,890 nuclei in late-stage Alzheimer’s Disease (AD), accessible through our intuitive web portal, profiling chromatin accessibility and gene expression in the same biological samples and uncovering vast cellular heterogeneity. We identified cell-type specific, disease-associated candidate cis-regulatory elements and their candidate target genes, including an oligodendrocyte-associated regulatory module containing links to APOE and CLU. We describe cis-regulatory relationships in specific cell-types at AD risk loci defined by genome wide association studies (GWAS), demonstrating the utility of this multi-omic single-nucleus approach. Trajectory analysis of glial populations identified disease-relevant transcription factors, like SREBF1 and their regulatory targets. Further, we introduce scWGCNA, a co-expression network analysis strategy robust to the sparsity of single-cell data, to perform a systems-level meta-analysis of AD transcriptomics.

overall_design: A multi-omics analysis of Alzheimer's Disease in human postmortem brain tissue using single-nucleus ATAC-seq and RNA-seq (bulk and single-nucleus).

first: Samuel

last: Morabito

first: Emily

last: Miyoshi


title: shRNA mediated PAR1 downregulation in PANC-1 cell line

city: Amsterdam

first: Cansu

last: Tekin

state: Noord-Holland

address: Meibergdreef 9, G2-132, P.O. Box 22660

country: Netherlands

institute: Amsterdam University Medical Center

summary: shRNA against PAR1 and control haripin sh004 transduced PANC-1(Pancreatic cancer) cell line

overall_design: For lentiviral silencing of PARq in the human PDAC cell line PANC-1, MISSION shRNA library (Sigma-Aldrich, St. Louis, MO) clone TRCN0000003690 was used. Clone shc004 was used as control

first: Brendon

last: Scicluna

first: Maarten

last: Bijlsma

first: C

last: Spek


title: Expression Data from Arabidopsis axs1-1 axs2-1/+ mutant

first: Xianhai

last: Zhao

address: Wushan

department: College of Forestry and Landscape Architecture

institute: South China Agricultural University

summary: Microarray analysis was performed on seedling roots of wild-type Col-0 and axs1-1 axs2-1/+ mutant

overall_design: RNA was prepared from the roots of 12 dpg seedlings of axs1-1 axs2-1/+ mutants and wild type plants and subjected to transcriptional profiling.

first: Ai-min

last: Wu


title: Tim-4+ Cavity-Resident Macrophages Impair Anti-Tumor CD8+ T cell Immunity [RNA-Seq]

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Here we report RNA sequencing data from sorted Tim-4low vs Tim-4high macrophages in steady-state (no tumor) mice and also MC38-LG-tumor-bearing animals that were treated with isotype or anti-Tim-4 antibody.

overall_design: Bulk RNA sequencing of sorted macrophages in triplicates

first: Andrew

last: Chow

first: Sara

last: Schad

first: Michael

middle: D

last: Green

first: Matthew

last: Hellmann

first: Viola

last: Allaj

first: Nicholas

last: Ceglia

first: Giulia

last: Zago

first: Nisargbhai

middle: S

last: Shah

first: Sai

last: Sharma

first: Marissa

last: Mattar

first: Joseph

last: Chan

first: Hira

last: Rizvi

first: Hong

last: Zhong

first: Cailian

last: Liu

first: Yonina

last: Bykov

first: Dmitriy

last: Zamarin

first: Hongyu

last: Shi

first: Sadna

last: Budhu

first: Corrin

last: Wohlhieter

first: Fathema

last: Uddin

first: Aditi

last: Gupta

first: Inna

last: Khodos

first: Jessica

last: Waninger

first: Angel

last: Qin

first: Geoffrey

last: Markowitz

last: Mittal

first: Vinod

last: Balachandran

middle: N

last: Durham

first: Dung

last: Le

first: Weiping

last: Zou

first: Sohrab

last: McPherson

first: Katherine

last: Panageas

first: Jason

last: Lewis

first: Justin

last: Perry

first: Elisa

last: de Stanchina

first: Triparna

last: Sen

first: John

last: Poirier

first: Jedd

last: Wolchok

first: Charles


title: Expression data from resting and activated murine T cell as well as murine peripheral T cell lymphomas

status: Public on May 11 2021

city: Oullins

first: GENESTIER

last: Laurent

address: Faculté de Medecine Lyon Sud. 165 Chemin du petit Revoyet

institute: INSERM

summary:
Peripheral T-cell lymphomas (PTCLs) represent a significant unmet medical need with dismal clinical outcome.T-cell receptor (TCR) is emerging as a key driver of T lymphocytes transformation. However, the role of chronic TCR activation in lymphomagenesis and in survival of lymphoma cells is still poorly understood. Using an original mouse model, we report here that chronic TCR stimulation drives T-cell lymphomagenesis whereas TCR signaling does not contribute to PTCL survival.
Transcriptome analyses of mouse PTCLs revealed a NK-like reprogramming of PTCL cells with expression of NK receptors (NKRs) and downstream signaling molecules such as Tyrobp and Syk.

overall_design: 15 samples. 9 mPTCLs generated after transfert of p53KO T cells into syngeneic recipient C57BL/6 CD3KO mice and 6 control T cells (3 repetitions of resting T cells and 3 repetitions of in vitro activated p53KO T cells)

first: Sylvain

last: Carras

first: Emmanuel

last: Bachy

first: Laurent

last: Genestier


title: Tim-4+ Cavity-Resident Macrophages Impair Anti-Tumor CD8+ T cell Immunity

city: New York

first: Bic

last: MSKCC

overall_design: Refer to individual Series


title: Tim-4+ Cavity-Resident Macrophages Impair Anti-Tumor CD8+ T cell Immunity [scRNA-Seq]

summary: Here we report transcriptional and TCR specificities associated with PSlow and PShigh CD8 T cells.

overall_design: Single cell TCR/RNA sequencing was performed on sorted PSlow and PShigh CD8 T cells from five MC38-LG bearing mice that had been treated with anti-Tim-4 and anti-PD-1. Cells from the individual mice were hashtagged to allow subsequent deconvolution.

first: Andrew

last: Chow

first: Sara

last: Schad

first: Michael

last: Green

first: Matthew

last: Hellmann

first: Viola

last: Allaj

first: Nicholas

last: Ceglia

first: Giulia

last: Zago

first: Nisargbhai

last: Shah

first: Sai

last: Sharma

first: Marissa

last: Mattar

first: Joseph

last: Chan

first: Hira

last: Rizvi

first: Hong

last: Zhong

first: Cailian

last: Liu

first: Yonina

last: Bykov

first: Dmitriy

last: Zamarin

first: Hongyu

last: Shi

first: Sadna

last: Budhu

first: Corrin

last: Wohlhieter

first: Fathema

last: Uddin

first: Aditi

last: Gupta

first: Inna

last: Khodos

first: Jessica

last: Waninger

first: Angel

last: Qin

first: Geoffrey

last: Markowitz

first: Vivek

last: Mittal

first: Vinod

last: Balachandran

first: Jennifer

middle: T


title: Methylation of Dual Specificity Phosphatase 4 Controls Cell Differentiation

first: Minkui

last: Luo

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Mitogen-activated protein kinases are inactivated by dual specificity phosphatases (DUSPs), whose activities are tightly regulated during cell differentiation. Using knockdown screening and single-cell transcriptional analysis, we determined that DUSP4 is the phosphatase that specifically inactivates p38 kinase for the promotion of megakaryocyte (Mk) differentiation. Mechanistically, PRMT1-mediated methylation of DUSP4 triggers its ubiquitinylation by an E3 ligase HUWE1. Interestingly, the mechanistic axis of the DUSP4 degradation and p38 activation is also associated with a transcriptional signature of immune activation in Mk cells. In the context of thrombocytopenia observed in myelodysplastic syndromes (MDS), we demonstrated that high levels of p38 MAPK and PRMT1 are associated with low platelet counts and adverse prognosis, while pharmacological inhibition of p38 MAPK or PRMT1 stimulates megakaryopoiesis. These findings provide mechanistic insights into the role of the PRMT1-DUSP4-p38 axis on Mk differentiation and present a targeting strategy for treatment of thrombocytopenia associated with MDS.

overall_design: Human bone marrow-derived CD34+ cells were cultured in a prestimulation medium (IMDM + 20% BIT + Basic Cytokine Mix: 100 ng/mL SCF, 20 ng/mL TPO, 100 ng/mL FLT3 Ligand and 50 ng/mL IL-6) for four days and examined for the surface markers CD41a/CD42b before processing for scRNA-seq. For un-stimulated cells (Sample 1 in Figure 4), approximately 100,000 cells were harvested. The rest of CD34+ cells were cultured in a Mkstimulating medium (IMDM + 20% BIT + MK Cytokine Mix: 25 ng/mL SCF, 50 ng/mL TPO), which was replaced with fresh Mk-stimulating medium on Day 4 and Day 7. On Day 8 poststimulation, approximately 100,000 cells were collected as TPO/SCF-stimulated cells (Sample 2 in Figure 4).  FACS sorting of the TPO/SCF-stimulated cells allowed the collection of approximately 88,000 TPO/SCF-stimulated, CD41a+CD42b+ cells (Sample 4 in Figure 4) and 100,000 TPO/SCF-stimulated, non-CD41a+CD42b+ cells (Sample 3 in Figure 4). The four sets of cell samples were immediately subject to Drop-Seq-based single cell RNA sequencing as detailed below.

first: Ming

last: Jiang


title: Retinoblastoma from Human Stem Cell-Derived Retinal Organoids

city: Memphis

first: Michael

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital


title: Retinoblastoma from Human Stem Cell-Derived Retinal Organoids (BeadChIP)

summary: Retinoblastoma is a childhood cancer of the developing retina that initiates with biallelic inactivation of the RB1 gene. To develop a laboratory model of human retinoblastoma formation, we made induced pluripotent stem cells (iPSCs) from 15 participants with germline RB1 mutations. After 45 days in culture, the retinal organoids were dissociated and injected into the vitreous of eyes of immunocompromised mice to support retinoblastoma tumor growth. Retinoblastomas formed from retinal organoids made from patient-derived iPSCs had molecular, cellular and genomic features indistinguishable from human retinoblastomas.

overall_design: We made induced pluripotent stem cells (iPSCs) from 15 participants with germline RB1 mutations. After 45 days in culture, the retinal organoids were dissociated and injected into the vitreous of eyes of immunocompromised mice to support retinoblastoma tumor growth. We validated tumors by comparing whole genome sequencing, RNA-sequencing, methylation analysis, and single cell sequencing of organoid derived tumors to patient tumors and patient derived xenografts.

first: Jackie

last: Norrie


title: RNA sequencing analysis of lung samples of control and irradiated animals

city: Winston-Salem

first: J. Mark

last: Thakur

state: North Carolina

address: Medical Center Boulevard

department: Pathology-Comparative Medicine

institute: Wake Forest School of Medicine

summary: Purpose: Radiation-induced lung injury (RILI) is a progressive condition, with an early phase, radiation pneumonitis (RP), and a late phase, lung fibrosis (LF). RILI may occur after partial body ionizing radiation exposures or by internal radioisotope exposure, with wide individual variability in timing and extent of lung injury. This study aims to provide new insights into the pathogenesis and progression of RILI in the non-human primate (NHP) rhesus macaque model. Methods:We used an integrative approach to understand RILI and its evolution at clinical and molecular levels in seventeen NHPs exposed to10 Gy of whole thorax irradiation in comparison to three sham-irradiated control NHPs. Lung samples were collected at necropsy for molecular and histopathological analyses using RNA sequencing and immunohistochemistry Results: Our data enhances understanding of RILI in non-survivors and survivors in a NHP model. RNA sequencing highlighted the role of SERPINA3, ATP12A, GJB2, CLDN10, TOX3, LPA as possible biomarkers and potential therapeutic targets of RILI. Their differential expression in nonsurvivors and survivors correlated with the severity of the disease.

overall_design: Snap frozen lung samples were selected from 3 lung regions (per animal) from  4 irradiated non-survivor animals (total 12 samples), 4 irradiated survivor animals (total 12 samples)  and 2 regions (per animal) from 3 control animals (total 6 samples) for RNA extraction and sequencing.

first: Priyanka

first: J

middle: M

last: Cline


title: Retinoblastoma from Human Stem Cell-Derived Retinal Organoids (RNA-Seq)

middle: A


title: The nascent m6A methylome in human cells

city: HOUSTON

first: Ruoyu

last: Wang

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

type: Methylation profiling by high throughput sequencing

summary: Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes and nucleate a dozen RNA binding proteins (RBPs) that are putative novel m6A readers, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes, where they act as transcriptional ‘roadblock’ to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription.

overall_design: The lanscape of m6A methylation on nascent RNAs in human cells

first: Wenbo

last: Li

first: Feng

last: Xiong


title: Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at CpG islands

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr Penfield Ave

department: Human Genetics

institute: McGill University

summary: Precise deposition of CpG methylation is critical for mammalian development and tissue homeostasis and is often dysregulated in human diseases. The localization of de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is facilitated by PWWP domain recognition of histone H3 lysine 36 (H3K36) methylation (Baubec et al. 2015, Weinberg et al. 2019) and is normally excluded from CpG islands (CGIs) (Wu et al. 2010). However, CpG methylation of CGIs that are regulated by Polycomb repressive complexes (PRCs) has been observed during embryogenesis (Chen et al. 2019), cellular differentiation (Mohn et al. 2008), and cancer progression (Ohm et al. 2007, Schlesinger et al. 2007, Widschwendter et al. 2007), suggesting that an uncharacterized mechanism exists to compete for de novo DNMT recruitment. Here we report that DNMT3A PWWP domain mutations recently identified in paragangliomas (Remacha et al. 2018) and microcephalic dwarfism (Heyn et al. 2019) promote localization of DNMT3A to CGIs in a PRC1-dependent manner. Genome-wide analysis shows that DNMT3A PWWP mutants redistribute to regions containing ubiquitylation of histone H2A at lysine 119 (H2AK119Ub) deposited by PRC1, irrespective of the levels of PRC2-catalyzed tri-methylation of histone H3 at lysine 27 (H3K27me3). DNMT3A, but not DNMT3B, is capable of directly interacting with H2AK119Ub-modified nucleosomes through a putative amino-terminal ubiquitin-dependent recruitment (UDR) region, which serves as an alternative form of genomic targeting in cells upon loss of PWWP reader function. Ablation of PRC1 abrogates localization of DNMT3A PWWP mutants to CGIs and prevents aberrant hypermethylation at these sites. Our study implies that a balance between DNMT3A recruitment by distinct reader domains guides de novo CpG methylation and may underlie the abnormal DNA methylation landscapes observed in human cancers and developmental disorders.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: ChIP-seq for DNMT3A1 variants and histone H3 post-translational modifications, and RRBS in parental C3H10T1/2 cells. ChIP-seq for DNMT3A1 variants, ChIP-Rx (Drosophila spike-in) for H2AK119Ub, and H3K27me3, and RRBS in sgRing1a/b C3H10T1/2 cells.

first: Daniel

last: Weinberg

first: Phillip

last: Rosenbaum

first: Xiao

last: Chen

first: Douglas

last: Barrows

first: Cynthia

last: Horth

first: Matt

middle: R

last: Marunde

first: Zachary

middle: B

last: Gillespie

first: Michael-Christopher

last: Keogh

first: Chao

last: Lu

first: Charles

last: Allis


title: Functional role of CPPED1 in trophoblasts.

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

summary: Analysis of the effect of CPPED1 siRNA experiment with and without P4

overall_design:
RNA-seq analysis of silenced CPPED1 (n = 3) and negative control (n=3) samples, and the samples treated with P4 (in EtOH) or EtOH
This submission is part of the study of which the first part is already submitted under GSE103035 accession number

first: Ravindra

last: Daddali


title: lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Probe SLERT secondary structure by SHAPE-MaP in PA1 cell line

overall_design: SHAPE-MaP of in vivo SLERT

first: Man

last: Wu

first: Guang

last: Xu

first: Chong

last: Han

first: Fang

first: Ling-Ling


title: Natural Mucosal Barriers and COVID-19 in Children

city: Bronx

first: Betsy

last: Herold

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary:
BACKGROUND. Coronavirus disease 2019 (COVID-19) is more benign in children compared with adults for unknown reasons. This contrasts with other respiratory viruses where disease manifestations are often more severe in children. We hypothesize that a more robust early innate immune response to SARS coronavirus 2 (SARS-CoV-2) protects against severe disease.
METHODS. Clinical outcomes, SARS-CoV-2 viral copies, and cellular gene expression were compared in nasopharyngeal swabs obtained at the time of presentation to the emergency department from 12 children and 27 adults using bulk RNA sequencing and quantitative reverse-transcription PCR. Total protein, cytokines, and anti–SARS-CoV-2 IgG and IgA were quantified in nasal fluid. We used a subset of 21 samples for RNAseq analysis.
RESULTS. SARS-CoV-2 copies, angiotensin-converting enzyme 2 (ACE2), and TMPRSS2 gene expression were similar in children and adults, but children displayed higher expression of genes associated with IFN signaling, NLRP3 inflammasome, and other innate pathways. Higher levels of IFN-α2, IFN-γ, IP-10, IL-8, and IL-1β protein were detected in nasal fluid in children versus adults. Children also expressed higher levels of genes associated with immune cells, whereas expression of those associated with epithelial cells did not differ in children versus adults. Anti–SARS-CoV-2 IgA and IgG were detected at similar levels in nasal fluid from both groups. None of the children required supplemental oxygen, whereas 7 adults did (P = 0.03); 4 adults died.
CONCLUSION. These findings provide direct evidence of a more vigorous early mucosal immune response in children compared with adults and suggest that this contributes to favorable clinical outcomes.

overall_design: 21 samples from pediatric and adult patients were included in the RNAseq cohort.

first: Carl

last: Pierce

first: Kevan


title: Genome-wide CRISPR screening reveals nucleotide synthesis negatively regulates autophagy

city: Tokyo

first: Noboru

last: Mizushima

address: 7-3-1 Hongo

institute: The University of Tokyo

summary: Macroautophagy (hereafter, autophagy) is a process that directs the degradation of cytoplasmic material in lysosomes. In addition to its homeostatic roles, autophagy undergoes dynamic positive and negative regulation in response to multiple forms of cellular stress, thus enabling the survival of cells. However, the precise mechanisms of autophagy regulation are not fully understood. To identify potential negative regulators of autophagy, we performed a genome-wide CRISPR screen using the quantitative autophagic flux reporter GFP-LC3-RFP. We identified phosphoribosylformylglycinamidine synthase (PFAS), a component of the de novo purine synthesis pathway, as one such negative regulator of autophagy. Autophagy was activated in cells lacking PFAS or phosphoribosyl pyrophosphate amidotransferase (PPAT), another de novo purine synthesis enzyme, or treated with methotrexate when exogenous levels of purines were insufficient. Purine starvation-induced autophagy activation was concomitant with mTORC1 suppression, and was profoundly suppressed in cells deficient for TSC2, which negatively regulates mTORC1 through inhibition of RHEB, suggesting that purines regulate autophagy through the TSC-RHEB-mTORC1 signaling axis. Moreover, depletion of the pyrimidine synthesis enzymes carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD) and dihydroorotate dehydrogenase (DHODH) activated autophagy as well, although mTORC1 activity was not altered by pyrimidine shortage. These results suggest a different mechanism of autophagy induction between purine and pyrimidine starvation. These findings provide novel insights into the regulation of autophagy by nucleotides and possibly the role of autophagy in nucleotide metabolism, leading to further developing anticancer strategies involving nucleotide synthesis and autophagy.

overall_design: Genome-wide CRISPR screen of autophagy-activated cells, measured using the GFP-LC3-RFP autophagy flux reporter.

first: Kaito

last: Mimura

first: Jun-ichi

last: Sakamaki

first: Hideaki

last: Morishita

first: Masahito

last: Kawazu

first: Hiroyuki

last: Mano


title: HLADR expression marks recently divided memory CD4 T cells in latent tuberculosis infected subjects upon in vitro stimulation with Mycobacterium tuberculosis antigens

city: San Diego

first: Rashmi

last: Tippalagama

address: 9420 Athena Cir, La Jolla

department: Peters

institute: La Jolla Institute for immunology

summary: Upon antigen encounter, T cells can rapidly divide and form short-lived effector cells which plays an important role fighting an active infection. However, little is known about the molecular markers that distinguish such effector cells from other T cell populations in humans. Due to previous exposure with Mycobacterium tuberculosis (Mtb), we expect latent tuberculosis infected (LTBI) subjects to have Mtb-specific memory CD4 T cells that are capable of rapid expansion upon antigen re-encounter. To investigate this further we designed an in vitro MTP-AE (Memory T cell Proliferation upon Antigen Exposure) assay to track and isolate proliferated CD4 T cells in response to antigen stimulation. PBMCs from LTBI subjects were cultured with the MTB300 (Mtb specific peptide pool, PMID: 27409590) for 8 days before sorting for HLADR+ vs HLADR- and divided vs undivided CD4 T cells. We found that HLADR is a marker of recently divided memory CD4 T cells and that differentially expessed genes in HLADR+/recently divided cells were enriched for cytotoxic markers and cytokines compared to HLADR-/undivided cells.

overall_design: Bulk RNA-sequencing of sorted memory CD4 T cells based on HLADR expression (HLADR+/HLADR-) or based on Cell Trace Violet staining (undivided (Div0), cells that have undergone one division (Div1) and cells that have undergone at least two divisions (Div2)) after 8 days post in vitro stimulation of PBMCs from latent TB donors with DMSO, MTB300 (Mtb-specific peptide pool,PMID: 27409590)  or anti-CD3/CD28. Additionally, on D0 (ex vivo) and D1 (24 hrs post stimulation) memory CD4 T cells were directly sorted for bulk RNA-sequencing

first: Jason

last: Greenbaum

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette

first: Bjoern

last: Peters

first: Julie

last: Burel


title: Transcriptomic profile of circulating memory CD4 T cells in active versus latent tuberculosis

city: La Jolla

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: Tuberculosis (TB) is responsible for the majority of mortality and morbidity associated with infectious diseases worldwide. The characterization of exact molecular components of immune response associated with protection against TB may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of memory T cells associated with active versus latent infection with Mycobacterium tuberculosis. Transcriptomic profiling using RNA sequencing was performed on memory CD4 T cells isolated from individuals with active TB (at diagnosis and 2 months post treatment), latent TB, as well as from TB negative healthy controls. Overall, we found specific gene signatures for each cohort that could successfully discriminate between individuals with active TB at diagnosis, treated active TB, latent TB and healthy controls.

overall_design:
RNA-sequencing of sorted memory CD4 T cells from cryopreserved PBMC of 25 subjects with active tuberculosis a diagnosis (including 21 with an additional sample collected at 2 months post treatment), 40 subjects with latent tuberculosis infection and 20 tuberculosis negative healthy controls
Note: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns


title: Next generation sequencing to find new medical targets for the treatment of conduit stenosis

city: Goettingen

first: Gabriela

last: Salinas

address: Kreuzbergring 57

institute: Universitaetsmedizin Goettingen

summary: To find new medical tagets for the treatment of conduit stenosis, 11 pulmonary bioartificial valved conduits were explanted from patients with a congenital heart defect and next generation sequencing was performed using material from the thickened stenosis-causing conduit wall and the respective leaflet. Deregulated genes between 9 samples from the thickened conduit-wall and 8 leaflets were determined and all receptor tyrosin kinases were selected for further experiments.

overall_design: Next generation sequencing of mRNA from thickened wall tissue and leaflet material from stenosed explanted pulmonary valved conduits.

first: Orr

last: Shomroni

first: Katja

last: Eildermann

first: Rudi

last: Foth